Mosquito Metagenomics Summary

Links to Files

Some files generated are too large to store on GitHub (e.g., contig sequences, publication-quality images). Large files can be accessed from DropBox folders below:

Dropbox link to raw assemblies separated by sample

Dropbox link to raw assemblies concatenated into a .csv

Dropbox link to publication quality figures

Raw RNA sequencing reads can be retrieved from the NCBI short sequence read archive under the SRA accession number PRJNA793247.

Re-BLAST 2023

Due to the significant changes to GenBank we are re-BLASTing results. To speed things up, I am curating custom BLAST databases using sequences downloaded from GenBank’s Nucleotide database using Entrez Queries to eliminate sequences that are extremely unlikely to be present in our samples that make up a large portion of the Nucleotide database. BLAST is being run locally using CLC Genomics Workbench. I am BLASTing by taxon categories (e.g., viruses, fungi, parasites) as we are limited by computational availability. For example, eliminating the top few viruses (unlikely to be found in mosquitoes) in the nucleotide database reduces the number of sequences by 90%.

Viruses

Entrez Query:

Viruses [ORGN] NOT Coronavirus [ORGN] NOT Human immunodeficiency virus 1 [ORGN] NOT Influenza A virus [ORGN] NOT Hepacivirus C [ORGN] NOT Hepatitis B virus [ORGN] NOT Influenza B virus [ORGN] NOT Rotavirus A [ORGN] NOT Norwalk virus [ORGN] NOT Simian immunodeficiency virus [ORGN]

Re-BLAST 2023 Steps

1. Concatenate all read mapping data and contigs: 01 - Mappings & Contigs.R
2. Re-BLAST all contig sequences against local NCBI virus blast (curated via above Entrez Query) using CLC
3. Read local BLAST results and filter results: 02 - Read Nt Local BLAST.R
4. BLAST all contig sequences passing filters at NCBI against all organisms to eliminate false positives using CLC
5. Read BLAST at NCBI results and filter out non-virus sequences: 03 - BLAST at NCBI.R
6. tBLASTx on contig sequences passing filters from step using local database on CLC to determine aa identites
7. Read tBLASTx results and filter: 04 - tBLASTx.R

Non-Virus Sequences

Non-virus sequences (e.g., Fungi, parasites, bacteria, plants, vertebrates) were considerably lower in overall number as well as quality. Furthermore, for these reasons, it was difficult to discern species from the recovered sequences. Some of the reasons for this is that compared to viruses where often we recovered the near complete genome, for fungi, parasites, bacteria, plants and vertebrates we recovered mostly rRNA, mitochondrial sequences, or in the case of plants, chloroplast sequences. Therefore, we decided to conduct analyses for non-virus sequences recovered at a higher level (e.g., Family, Genus) rather than species. This still gives us a good idea about what organisms are harboured by mosquitoes.

Methods

Host and Quality Filtering

Chan Zuckerberg ID Metagenomic Pipeline v6.8 (Chan Zuckerberg Biohub; CZID), an open-sourced cloud-based bioinformatics platform (https://czid.org/) was used for quality control and host filtration of reads as well as de novo assembly and taxonomic binning as described by Batson et al., (2021) and Kalantar et al., (2020). The CZID pipeline employs STAR and Bowtie2 to perform host filtration (human and mosquito), Trimmomatic for adapter trimming, Price Seq for removal of low-quality reads, LZW for the removal of low complexity reads and CZIDdedup for duplicate read identification.

De Novo Assembly

The host and quality filtered reads were allowed to continue through the CZID pipeline, which involves de novo assembly with SPADES using default settings and only the assembly module. After assembly, reads are mapped back to contigs with Bowtie2. The host and quality filtered reads from CZID (the Bowtie2 output) were downloaded and assembled with the CLC Genomics Workbench version 20 assembler with a minimum contig length of 250 nt, mismatch cost of 2, insertion cost of 3, deletion cost of 3, length fraction of 0.7 and a similarity fraction of 0.95. Contigs were subject to BLASTn and tBLASTx searches on a custom NCBI viruses database using the above Entrez Query and the NCBI nt database. The BLAST results were very similar between CZID and CLC, thus we opted to use CLC Genomics Workbench version 20 for subsequent analyses.

BLAST

Assembled contigs were subject to BLASTn searches on the NCBI non-redundant nucleotide database, and contigs were assigned to taxa based on BLAST results. Positive contigs from BLASTn were subject to tBLASTx to identify amino acid identities. We were looking for non-mosquito sequences of viral, bacterial, parasitic, fungal and plant origin and discarded sequences that were of mosquito origin.

To begin, BLASTn search results were filtered by E-value (≤1x 10^-100) and contig length (≥250). Contigs with a match length of ≥250 nt, ≥90% for both nt and aa sequence similarity were classified as hits. Coverage depth was analyzed on a per-sequence basis: for viruses, we used a minimum threshold of 10X coverage depth, and we were less strict for protozoan, fungal, bacterial, plant and chordate coverage. For virus hits, contigs meeting these criteria were subject to tBLASTx searches to identify amino acid identities.

Contigs of viral origin with a percent nt identity <85% were flagged as potentially novel viruses. While the ICTV sets specific standards for different viral taxa for percent identity to claim a novel virus, many of the viruses we recovered are unclassified beyond the order or family classification, which can make selecting an identity threshold difficult. Therefore, we selected ≤85% as the cut-off because Kalantar et al., (2020) suggests that <90% nt identity is a good general threshold and we opted to be more conservative in our assignments of novel viruses.

Libraries

require(pacman)
pacman::p_load(tidyverse, janitor, here, DT, gt, phylotools, assertr, readxl, patchwork, reshape2, ggtext, openxlsx, grid, tiff)

Load Data

virus_master_2023 <- read_csv(here("Data/tblastx_master.csv"))

Sequencing Summary

# Read count & contigs
virus_master_2023 %>% 
  mutate(reads_log10 = log10(total_read_count)) %>% 
  drop_na(genome) %>% 
  ggplot(aes(x = contig_length, y = reads_log10)) +
  geom_point(aes(colour = genome)) +
  scale_colour_viridis_d("Genome") +
  theme_bw() +
  labs(x = "Contig Length (nt)",
       y = "Reads (Log 10)")

# Read count & contigs (mosquito species)

virus_master_2023 %>% 
  mutate(reads_log10 = log10(total_read_count)) %>% 
  drop_na(genome) %>% 
  ggplot(aes(x = contig_length, y = reads_log10)) +
  geom_point(aes(colour = mosquito_species)) +
  scale_colour_viridis_d("Species") +
  theme_bw() +
  labs(x = "Contig Length (nt)",
       y = "Reads (Log 10)")

# Contig length and coverage
virus_master_2023 %>% 
  mutate(coverage_log10 = log10(coverage)) %>% 
  ggplot(aes(x = contig_length, y = coverage_log10)) +
  geom_point(aes(colour = genome)) +
  scale_colour_viridis_d() +
  theme_bw() +
    labs(x = "Contig Length (nt)",
       y = "Coverage (Log 10)")

# Coverage reads

virus_master_2023 %>% 
  mutate(coverage_log10 = log10(coverage)) %>% 
  mutate(reads_log10 = log10(total_read_count)) %>% 
  ggplot(aes(x = coverage_log10, y = reads_log10)) +
  geom_point(aes(colour = genome)) +
  scale_colour_viridis_d("Genome") +
  theme_bw() +
  labs(x = "Coverage Depth (Log 10)",
       y = "Reads (Log 10)")

# Contig Length and % ID
virus_master_2023 %>% 
  ggplot(aes(x = contig_length, y = greatest_identity_percent)) +
  geom_point(aes(colour = genome)) +
  scale_colour_viridis_d() +
  theme_bw() +
  labs(x = "Contig Length (nt)",
       y = "Percent aa Identity")

BLAST Summary

library_summary <- virus_master_2023 %>%
  group_by(mosquito_species, sample_number) %>%
  summarise(n = n_distinct(mosquito_species)) %>%
  group_by(mosquito_species) %>%
  summarise(n = n()) %>%
  adorn_totals()

years <- virus_master_2023 %>% 
  group_by(collection_year, virus_name) %>% 
  summarise(count = n_distinct(virus_name, collection_year)) %>% 
  pivot_wider(names_from = collection_year, values_from = count, values_fill = 0)

virus_lineage <- virus_master_2023 %>% 
  group_by(virus_name, viral_family, genome) %>% 
  summarise(n = n_distinct(virus_name, viral_family, genome)) %>% 
  select(-"n")

virus_master_2023 %>% 
  group_by(virus_name) %>% 
  summarise(n_contigs = n(),
            mean_cov = mean(coverage),
            min_cov = min(coverage),
            max_cov = max(coverage),
            mean_pid = mean(greatest_identity_percent),
            med_pid = median(greatest_identity_percent),
            min_pid = min(greatest_identity_percent),
            max_pid = max(greatest_identity_percent),
            total_reads = sum(total_read_count),
            longest_contig = max(contig_length)) %>% 
  left_join(virus_lineage, by = "virus_name") %>% 
  group_by(genome, viral_family) %>% 
  arrange(genome, viral_family) %>% 
  relocate(total_reads, .after = "n_contigs") %>% 
  relocate(longest_contig, .after = "n_contigs") %>% 
  mutate(across(.cols = "virus_name",
                ~case_when(grepl("Manitoba", virus_name) & !grepl("Manitoba virus", virus_name) ~ 
                             paste0(., "*"),
                           TRUE ~ .))) %>% 
  gt() %>% 
  fmt_number(columns = mean_cov:max_pid,
             decimals = 2) %>% 
  fmt_number(columns = total_reads,
             sep_mark = ",",
             decimals = 0) %>% 
  tab_spanner(label = "Coverage Depth", columns = c(mean_cov, min_cov, max_cov)) %>% 
  tab_spanner(label = "aa Percent Identity", columns = c(mean_pid, min_pid, max_pid, med_pid)) %>% 
  cols_label(
    n_contigs = "Contigs",
    longest_contig = "Longest Contig (nt)",
    total_reads = "Reads",
    mean_cov = "Mean", min_cov = "Min", max_cov = "Max",
    mean_pid = "Mean", min_pid = "Min", max_pid = "Max", med_pid = "Median",
    virus_name = "Virus") %>% 
  tab_style(
    style = list(cell_fill(color = "grey"),
                 cell_text(weight = "bold")),
    locations = cells_row_groups(groups = everything())
  ) %>% 
  tab_style(
    style = cell_borders(
      sides = "left",
      weight = px(2),
      color = "grey"),
    locations = cells_body(
      columns = c(mean_cov, mean_pid, "n_contigs")
    )
  ) %>% 
  data_color(
    columns = mean_pid:max_pid,
    palette = "viridis"
    
  ) %>% 
  tab_footnote("* Putatively novel virus.")

Virus	Contigs	Longest Contig (nt)	Reads	Coverage Depth			aa Percent Identity
				Mean	Min	Max	Mean	Min	Max	Median
+ssRNA - Dicistroviridae
Black queen cell virus	2	6035	1,613	17.00	11.15	22.85	100.00	100.00	100.00	100.00
Manitoba dicistro-like virus 1*	1	7146	10,688	149.27	149.27	149.27	82.61	82.61	82.61	82.61
Soybean thrips dicistrovirus	11	9121	11,192	17.32	10.11	29.01	100.00	100.00	100.00	100.00
+ssRNA - Flaviviridae
Inari jingmenvirus	1	1267	139	11.02	11.02	11.02	100.00	100.00	100.00	100.00
Placeda virus	169	11737	106,682	90.37	10.02	1,114.82	97.87	86.24	100.00	98.55
+ssRNA - Iflaviridae
Cafluga virus	2	3426	976	20.82	19.41	22.24	99.77	99.55	100.00	99.77
Culex Iflavi-like virus 4	23	9811	13,815	22.81	10.65	58.90	99.81	96.20	100.00	100.00
Culex iflavilike virus 3	183	1824	266,451	284.65	18.65	1,269.06	99.49	94.19	100.00	100.00
Hanko iflavirus 1	30	9246	2,938,402	3,394.01	10.99	19,795.35	97.49	93.45	100.00	97.30
Hanko iflavirus 2	16	9206	19,456	93.72	18.50	208.48	97.05	89.58	100.00	100.00
Hubei arthropod virus 1	1	2967	352	11.95	11.95	11.95	100.00	100.00	100.00	100.00
Manitoba iflavirus 1*	13	2435	10,000	78.09	16.30	242.52	78.42	67.08	83.54	79.47
Manitoba picorna-like virus 1*	20	2114	15,071	70.96	18.52	207.10	81.99	73.93	84.96	83.10
Pedersore iflavirus	25	9899	39,865	28.41	10.35	266.71	93.47	89.14	100.00	93.38
Soybean thrips iflavirus 4	1	3835	636	16.60	16.60	16.60	100.00	100.00	100.00	100.00
Thrace picorna-like virus 1	2	1172	2,010	82.45	34.10	130.79	91.62	89.58	93.65	91.62
Yongsan picorna-like virus 1	64	4085	55,324	62.58	10.27	180.88	89.40	85.05	100.00	89.11
Yongsan picorna-like virus 2	4	9573	58,132	165.26	34.98	535.91	100.00	100.00	100.00	100.00
+ssRNA - Luteoviridae
Marma virus	23	3160	39,344	70.95	11.62	129.64	100.00	100.00	100.00	100.00
+ssRNA - Narnaviridae
Culex narnavirus 1	1	513	63	12.07	12.07	12.07	100.00	100.00	100.00	100.00
Manitoba narnavirus 1*	2	1760	391	18.77	13.02	24.52	80.59	80.29	80.89	80.59
+ssRNA - Negevirus
Big Cypress virus	3	9570	6,079	37.12	18.89	65.64	98.77	96.30	100.00	100.00
Bro virus	1	11375	3,826	33.85	33.85	33.85	90.00	90.00	90.00	90.00
Cordoba virus	14	5133	135,594	548.17	17.51	2,225.85	97.10	93.75	100.00	97.23
Manitoba mononega-like virus 1*	1	11180	6,558	59.07	59.07	59.07	73.21	73.21	73.21	73.21
Manitoba mononega-like virus 2*	1	2477	494	20.03	20.03	20.03	75.00	75.00	75.00	75.00
Manitoba mononega-like virus 3*	1	5456	2,317	42.65	42.65	42.65	78.57	78.57	78.57	78.57
Mekrijarvi Negevirus	6	9873	167,549	294.01	30.28	1,262.63	94.13	90.78	100.00	93.40
Utsjoki negevirus 3	2	989	416	21.12	18.00	24.24	99.02	99.01	99.03	99.02
+ssRNA - Nodaviridae
Hubei noda-like virus 12	2	4762	4,244	54.47	23.60	85.34	95.83	91.67	100.00	95.83
+ssRNA - Tombusviridae
Des Moines River virus	4	2361	35,117	486.06	34.94	897.17	100.00	100.00	100.00	100.00
Hubei mosquito virus 4	6	5103	2,919	16.68	10.02	39.59	96.50	92.65	100.00	95.70
Manitoba tombus-like virus 1*	5	2340	15,873	157.57	74.52	277.22	75.68	72.73	76.92	76.19
Tiger mosquito bi-segmented tombus-like virus	1	2351	13,049	557.41	557.41	557.41	100.00	100.00	100.00	100.00
+ssRNA - Tymoviridae
Hubei macula-like virus 3	8	6059	530,385	1,092.52	11.15	7,749.86	96.13	92.15	100.00	96.63
Manitoba tymo-like virus 1*	1	6302	1,482	23.67	23.67	23.67	66.79	66.79	66.79	66.79
+ssRNA - Virgaviridae
Hubei virga-like virus 2	6	947	505	13.26	10.94	15.50	99.04	96.27	100.00	100.00
Manitoba virgavirus 1*	1	1675	186	11.06	11.06	11.06	83.83	83.83	83.83	83.83
-ssRNA - Chuviridae
Chuvirus	39	6799	22,130	28.00	10.17	214.52	97.49	89.66	100.00	97.02
-ssRNA - Orthomyxoviridae
Astopletus virus	29	1044	5,975	32.63	10.91	107.95	99.06	95.77	100.00	100.00
Wuhan mosquito virus 6	101	2467	133,667	176.35	12.58	641.58	99.76	97.69	100.00	100.00
-ssRNA - Peribunyaviridae
Culex bunyavirus 2	19	1896	6,255	23.92	10.28	49.84	100.00	100.00	100.00	100.00
-ssRNA - Rhabdoviridae
Canya virus	9	2444	2,613	29.27	11.64	66.33	90.87	85.05	100.00	85.92
Culex Rhabdo-like virus	4	1973	807	14.68	10.87	23.28	100.00	100.00	100.00	100.00
Culex rhabdovirus	2	429	997	116.26	74.47	158.06	100.00	100.00	100.00	100.00
Elisy virus	21	1817	3,849	19.29	10.10	40.69	99.27	96.41	100.00	100.00
Flanders hapavirus	81	8773	104,235	113.05	10.00	686.87	99.90	95.96	100.00	100.00
Manitoba Rhabdovirus 1*	20	5085	13,911	26.41	10.21	68.72	77.30	69.42	83.33	77.90
Manitoba rhabdovirus 2*	1	4648	2,401	51.70	51.70	51.70	75.00	75.00	75.00	75.00
Manitoba rhabdovirus 3*	5	6071	1,153	16.51	11.30	23.92	80.94	66.04	84.85	84.62
Manitoba virus	5	1589	1,003	19.71	15.74	24.80	99.76	98.80	100.00	100.00
Merida virus	55	7483	76,697	91.60	11.06	276.87	99.86	97.14	100.00	100.00
Riverside virus 1	17	8033	18,623	45.08	10.80	120.41	90.20	85.32	93.01	90.00
dsDNA - Iridoviridae
Manitoba iridescent virus 1*	1	797	137	16.99	16.99	16.99	78.74	78.74	78.74	78.74
dsRNA - Birnaviridae
Ballard Lake virus	48	3472	682,541	431.81	10.84	2,260.59	99.86	93.27	100.00	100.00
dsRNA - Partitiviridae
Partitivirus-like Culex mosquito virus	12	1751	4,477	23.28	11.49	45.83	100.00	100.00	100.00	100.00
dsRNA - Totiviridae
Gouley virus	3	368	117	12.22	10.42	14.89	95.04	92.86	97.67	94.59
Hattula totivirus 1	1	4909	702	14.41	14.41	14.41	89.07	89.07	89.07	89.07
Manitoba toti-like virus 1*	5	8930	13,869	39.82	11.18	127.46	69.92	67.43	73.11	68.10
Manitoba toti-like virus 2*	1	3123	418	13.45	13.45	13.45	60.24	60.24	60.24	60.24
Manitoba toti-like virus 3*	4	4626	1,772	15.11	11.20	18.40	73.53	72.22	74.90	73.50
Snelk virus	4	295	496	41.15	23.15	67.61	100.00	100.00	100.00	100.00
ssDNA - Parvoviridae
Aedes albopictus densovirus	4	3355	14,051	139.82	94.27	203.18	97.46	89.86	100.00	100.00
Aedes vexans densovirus isolate	1	3367	594	17.69	17.69	17.69	100.00	100.00	100.00	100.00
Culex densovirus	8	1697	6,035	127.22	11.65	490.03	99.56	97.71	100.00	100.00
Grus japonensis parvoviridae	1	570	366	60.82	60.82	60.82	100.00	100.00	100.00	100.00
* Putatively novel virus.

Virus Detections by Species

virus_master_2023 %>% 
  group_by(mosquito_species, virus_name) %>% 
  summarise(count = n_distinct(virus_name, sample_number)) %>% 
  pivot_wider(names_from = mosquito_species, values_from = count, values_fill = 0) %>% 
  mutate("Aedes canadensis \n Total: 1" = (`Aedes canadensis` / 1) * 100,
         "Aedes vexans \n Total: 19" = (`Aedes vexans` / 19) * 100,
         "Anopheles earlei \n Total: 1" = (`Anopheles earlei` / 1) * 100,
         "Coquillettidia perturbans \n Total: 6" = (`Coquillettidia perturbans` / 6) * 100,
         "Culex tarsalis \n Total: 11" = (`Culex tarsalis` / 11) * 100,
         "Ochlerotatus dorsalis \n Total: 5" = (`Ochlerotatus dorsalis` / 5) * 100,
         "Ochlerotatus flavescens \n Total: 1" = (`Ochlerotatus flavescens` / 1) * 100,
         "Ochlerotatus triseriatus \n Total: 1" = (`Ochlerotatus triseriatus` / 1) * 100,
  ) %>% select(-`Aedes canadensis`:-`Ochlerotatus triseriatus`) %>% 
  left_join(virus_lineage, by = "virus_name") %>% 
   left_join(years, by = "virus_name") %>% 
   relocate("2020", .after = "virus_name") %>% relocate("2021", .after = "2020") %>% 
   mutate(across(.cols = c("2020", "2021"),
                 ~case_when(. == "1" ~ TRUE,
                            . == "0" ~ FALSE))) %>% 
   mutate(across(.cols = "virus_name",
                 ~case_when(grepl("Manitoba", virus_name) & !grepl("Manitoba virus", virus_name) ~ 
                              paste0(., "*"),
                            TRUE ~ .))) %>% 
  group_by(genome, viral_family) %>% 
  arrange(genome, viral_family) %>% 
  gt() %>% 
  fmt_number(columns = "Aedes canadensis \n Total: 1":"Ochlerotatus triseriatus \n Total: 1",
             decimals = 2) %>% 
  tab_spanner(label = "Percent of Libraries Detected by Species", 
              columns = c("Aedes canadensis \n Total: 1":"Ochlerotatus triseriatus \n Total: 1")) %>% 
   tab_spanner(label = html("Years Detected"),
               columns = c("2020":"2021")) %>% 
  cols_label(
    "Aedes canadensis \n Total: 1" = html("<em>Aedes canadensis</em> <br> Total: 1"),
    "Aedes vexans \n Total: 19" = html("<em>Aedes vexans</em> <br> Total: 19"),
    "Anopheles earlei \n Total: 1" = html("<em>Anopheles earlei</em> <br> Total: 1"),
    "Coquillettidia perturbans \n Total: 6" = html("<em>Coquillettidia perturbans</em> <br> Total: 6"),
    "Culex tarsalis \n Total: 11" = html("<em>Culex tarsalis</em> <br> Total: 11"),
    "Ochlerotatus dorsalis \n Total: 5" = html("<em>Ochlerotatus dorsalis</em> <br> Total: 5"),
    "Ochlerotatus flavescens \n Total: 1" = html("<em>Ochlerotatus flavescens</em> <br> Total: 1"),
    "Ochlerotatus triseriatus \n Total: 1" = html("<em>Ochlerotatus triseriatus</em> <br> Total: 1"),
    virus_name = "Virus") %>% 
   cols_align(align = "center",
              columns = "2020":"Ochlerotatus triseriatus \n Total: 1") %>% 
   tab_style(
     style = list(cell_fill(color = "grey"),
                  cell_text(weight = "bold")),
     locations = cells_row_groups(groups = everything())) %>% 
   data_color(columns = `Aedes canadensis \n Total: 1`:last_col(),
              palette = "viridis", 
              direction = "row") %>% 
   tab_style(
     style = cell_borders(
       sides = "left",
       weight = px(2),
       color = "black"),
     locations = cells_body(
       columns = c("Aedes canadensis \n Total: 1"))) %>% 
  tab_footnote("* Putatively novel virus") %>% 
  tab_options(., container.width = 1500)

Virus	Years Detected		Percent of Libraries Detected by Species
	2020	2021	Aedes canadensis Total: 1	Aedes vexans Total: 19	Anopheles earlei Total: 1	Coquillettidia perturbans Total: 6	Culex tarsalis Total: 11	Ochlerotatus dorsalis Total: 5	Ochlerotatus flavescens Total: 1	Ochlerotatus triseriatus Total: 1
+ssRNA - Dicistroviridae
Black queen cell virus	TRUE	FALSE	0.00	5.26	0.00	0.00	0.00	0.00	0.00	0.00
Soybean thrips dicistrovirus	TRUE	TRUE	0.00	15.79	0.00	0.00	45.45	20.00	0.00	0.00
Manitoba dicistro-like virus 1*	TRUE	FALSE	0.00	0.00	0.00	0.00	9.09	0.00	0.00	0.00
+ssRNA - Flaviviridae
Inari jingmenvirus	TRUE	FALSE	0.00	5.26	0.00	0.00	0.00	0.00	0.00	0.00
Placeda virus	TRUE	TRUE	0.00	10.53	0.00	0.00	100.00	0.00	0.00	0.00
+ssRNA - Iflaviridae
Hanko iflavirus 1	TRUE	TRUE	0.00	21.05	0.00	16.67	9.09	100.00	100.00	0.00
Hanko iflavirus 2	TRUE	TRUE	0.00	57.89	0.00	16.67	0.00	20.00	0.00	0.00
Hubei arthropod virus 1	FALSE	TRUE	0.00	5.26	0.00	0.00	0.00	0.00	0.00	0.00
Manitoba iflavirus 1*	TRUE	TRUE	0.00	47.37	0.00	0.00	0.00	20.00	0.00	0.00
Manitoba picorna-like virus 1*	TRUE	TRUE	0.00	63.16	0.00	0.00	0.00	0.00	0.00	0.00
Pedersore iflavirus	TRUE	TRUE	0.00	36.84	0.00	33.33	27.27	80.00	100.00	0.00
Thrace picorna-like virus 1	FALSE	TRUE	0.00	10.53	0.00	0.00	0.00	0.00	0.00	0.00
Yongsan picorna-like virus 1	TRUE	TRUE	0.00	94.74	0.00	0.00	0.00	60.00	0.00	0.00
Cafluga virus	TRUE	FALSE	0.00	0.00	0.00	16.67	0.00	20.00	0.00	0.00
Soybean thrips iflavirus 4	TRUE	FALSE	0.00	0.00	0.00	16.67	0.00	0.00	0.00	0.00
Culex Iflavi-like virus 4	TRUE	TRUE	0.00	0.00	0.00	0.00	63.64	0.00	0.00	0.00
Culex iflavilike virus 3	TRUE	TRUE	0.00	0.00	0.00	0.00	100.00	0.00	0.00	0.00
Yongsan picorna-like virus 2	TRUE	TRUE	0.00	0.00	0.00	0.00	27.27	0.00	0.00	0.00
+ssRNA - Luteoviridae
Marma virus	TRUE	TRUE	0.00	0.00	0.00	16.67	100.00	0.00	0.00	0.00
+ssRNA - Narnaviridae
Manitoba narnavirus 1*	FALSE	TRUE	0.00	0.00	100.00	0.00	0.00	0.00	0.00	0.00
Culex narnavirus 1	TRUE	FALSE	0.00	0.00	0.00	0.00	9.09	0.00	0.00	0.00
+ssRNA - Negevirus
Bro virus	FALSE	TRUE	100.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
Manitoba mononega-like virus 1*	FALSE	TRUE	100.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
Manitoba mononega-like virus 2*	FALSE	TRUE	100.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
Big Cypress virus	TRUE	TRUE	0.00	15.79	0.00	0.00	0.00	0.00	0.00	0.00
Cordoba virus	FALSE	TRUE	0.00	15.79	0.00	0.00	0.00	0.00	0.00	0.00
Mekrijarvi Negevirus	TRUE	TRUE	0.00	15.79	0.00	0.00	0.00	60.00	0.00	0.00
Utsjoki negevirus 3	TRUE	FALSE	0.00	10.53	0.00	0.00	0.00	0.00	0.00	0.00
Manitoba mononega-like virus 3*	TRUE	FALSE	0.00	0.00	0.00	0.00	0.00	0.00	0.00	100.00
+ssRNA - Nodaviridae
Hubei noda-like virus 12	FALSE	TRUE	0.00	0.00	0.00	16.67	9.09	0.00	0.00	0.00
+ssRNA - Tombusviridae
Des Moines River virus	TRUE	FALSE	0.00	5.26	0.00	0.00	27.27	0.00	0.00	0.00
Hubei mosquito virus 4	TRUE	TRUE	0.00	0.00	0.00	0.00	54.55	0.00	0.00	0.00
Manitoba tombus-like virus 1*	TRUE	TRUE	0.00	0.00	0.00	0.00	45.45	0.00	0.00	0.00
Tiger mosquito bi-segmented tombus-like virus	FALSE	TRUE	0.00	0.00	0.00	0.00	9.09	0.00	0.00	0.00
+ssRNA - Tymoviridae
Hubei macula-like virus 3	TRUE	TRUE	0.00	21.05	0.00	0.00	0.00	20.00	0.00	0.00
Manitoba tymo-like virus 1*	FALSE	TRUE	0.00	5.26	0.00	0.00	0.00	0.00	0.00	0.00
+ssRNA - Virgaviridae
Hubei virga-like virus 2	TRUE	TRUE	0.00	0.00	0.00	0.00	36.36	0.00	0.00	0.00
Manitoba virgavirus 1*	TRUE	FALSE	0.00	0.00	0.00	0.00	0.00	20.00	0.00	0.00
-ssRNA - Chuviridae
Chuvirus	TRUE	TRUE	0.00	89.47	0.00	0.00	9.09	60.00	0.00	0.00
-ssRNA - Orthomyxoviridae
Wuhan mosquito virus 6	TRUE	TRUE	0.00	10.53	0.00	16.67	100.00	0.00	0.00	0.00
Astopletus virus	TRUE	TRUE	0.00	0.00	0.00	0.00	100.00	0.00	0.00	0.00
-ssRNA - Peribunyaviridae
Culex bunyavirus 2	TRUE	TRUE	0.00	0.00	0.00	0.00	100.00	0.00	0.00	0.00
-ssRNA - Rhabdoviridae
Manitoba rhabdovirus 3*	TRUE	TRUE	100.00	0.00	0.00	0.00	36.36	0.00	0.00	0.00
Flanders hapavirus	TRUE	TRUE	0.00	15.79	0.00	0.00	90.91	0.00	0.00	0.00
Manitoba Rhabdovirus 1*	TRUE	TRUE	0.00	73.68	0.00	0.00	0.00	20.00	0.00	0.00
Manitoba rhabdovirus 2*	TRUE	FALSE	0.00	5.26	0.00	0.00	0.00	0.00	0.00	0.00
Riverside virus 1	TRUE	TRUE	0.00	73.68	0.00	0.00	0.00	20.00	0.00	0.00
Canya virus	TRUE	TRUE	0.00	0.00	0.00	0.00	63.64	0.00	0.00	0.00
Culex Rhabdo-like virus	TRUE	TRUE	0.00	0.00	0.00	0.00	27.27	0.00	0.00	0.00
Culex rhabdovirus	FALSE	TRUE	0.00	0.00	0.00	0.00	18.18	0.00	0.00	0.00
Elisy virus	TRUE	TRUE	0.00	0.00	0.00	0.00	45.45	0.00	0.00	0.00
Manitoba virus	FALSE	TRUE	0.00	0.00	0.00	0.00	9.09	0.00	0.00	0.00
Merida virus	TRUE	TRUE	0.00	0.00	0.00	0.00	100.00	0.00	0.00	0.00
dsDNA - Iridoviridae
Manitoba iridescent virus 1*	FALSE	TRUE	0.00	0.00	0.00	16.67	0.00	0.00	0.00	0.00
dsRNA - Birnaviridae
Ballard Lake virus	TRUE	TRUE	0.00	100.00	0.00	66.67	18.18	20.00	0.00	0.00
dsRNA - Partitiviridae
Partitivirus-like Culex mosquito virus	TRUE	TRUE	0.00	0.00	0.00	0.00	100.00	0.00	0.00	0.00
dsRNA - Totiviridae
Manitoba toti-like virus 2*	FALSE	TRUE	100.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
Manitoba toti-like virus 1*	TRUE	TRUE	0.00	10.53	0.00	0.00	27.27	0.00	0.00	0.00
Gouley virus	TRUE	FALSE	0.00	0.00	0.00	0.00	27.27	0.00	0.00	0.00
Snelk virus	TRUE	TRUE	0.00	0.00	0.00	0.00	36.36	0.00	0.00	0.00
Manitoba toti-like virus 3*	TRUE	FALSE	0.00	0.00	0.00	0.00	0.00	80.00	0.00	0.00
Hattula totivirus 1	TRUE	FALSE	0.00	0.00	0.00	0.00	0.00	0.00	0.00	100.00
ssDNA - Parvoviridae
Aedes vexans densovirus isolate	FALSE	TRUE	0.00	5.26	0.00	0.00	0.00	0.00	0.00	0.00
Culex densovirus	TRUE	TRUE	0.00	5.26	0.00	66.67	9.09	0.00	0.00	0.00
Aedes albopictus densovirus	FALSE	TRUE	0.00	0.00	0.00	33.33	9.09	0.00	0.00	0.00
Grus japonensis parvoviridae	FALSE	TRUE	0.00	0.00	0.00	16.67	0.00	0.00	0.00	0.00
* Putatively novel virus

Viral Families

virus_master_2023 %>% 
  distinct(virus_name, viral_family, .keep_all = TRUE) %>% 
  group_by(genome, viral_family) %>% 
  summarise(n = n()) %>% 
  arrange(genome, n) %>%
  ggplot(aes(x = fct_inorder(viral_family), y = n)) +
  geom_col(aes(fill = genome)) +
  scale_fill_viridis_d("Genome") +
  scale_y_continuous(limits = c(0, 14), breaks = c(0, 2, 4, 6, 8, 10, 12, 14), expand = c(0,0)) +
  coord_flip() + 
  theme_bw() +
  labs(x = "Viral Family",
       y = "Number of Distinct Viruses Detected")

virus_master_2023 %>% 
  filter(novel_flag == "Not Novel") %>% 
  distinct(virus_name, viral_family, .keep_all = TRUE) %>% 
  group_by(genome, viral_family) %>% 
  summarise(n = n()) %>% 
  arrange(genome, n) %>%
  ggplot(aes(x = fct_inorder(viral_family), y = n)) +
  geom_col(aes(fill = genome)) +
  scale_fill_viridis_d("Genome") +
  scale_y_continuous(limits = c(0, 12), breaks = c(0, 2, 4, 6, 8, 10, 12), expand = c(0,0)) +
  coord_flip() + 
  theme_bw() +
  labs(x = "Viral Family",
       y = "Number of Distinct Viruses Detected")

virus_master_2023 %>% 
  filter(novel_flag != "Not Novel") %>% 
  distinct(virus_name, viral_family, .keep_all = TRUE) %>% 
  group_by(genome, viral_family) %>% 
  summarise(n = n()) %>% 
  arrange(genome, n) %>%
  ggplot(aes(x = fct_inorder(viral_family), y = n)) +
  geom_col(aes(fill = genome)) +
  scale_fill_viridis_d("Genome") +
  scale_y_continuous(limits = c(0, 4), breaks = c(0, 1, 2, 3, 4), expand = c(0,0)) +
  coord_flip() + 
  theme_bw() +
  labs(x = "Viral Family",
       y = "Number of Distinct Viruses Detected")

virus_master_2023 %>% 
  distinct(virus_name, viral_family, .keep_all = TRUE) %>% 
  group_by(genome, viral_family) %>% 
  summarise(n = n()) %>% 
  arrange(genome, desc(n)) %>% 
  adorn_totals() %>% 
  gt() %>% 
  cols_label(
    genome = "Genome",
    viral_family = "Family")

Genome	Family	n
+ssRNA	Iflaviridae	13
+ssRNA	Negevirus	8
+ssRNA	Tombusviridae	4
+ssRNA	Dicistroviridae	3
+ssRNA	Flaviviridae	2
+ssRNA	Narnaviridae	2
+ssRNA	Tymoviridae	2
+ssRNA	Virgaviridae	2
+ssRNA	Luteoviridae	1
+ssRNA	Nodaviridae	1
-ssRNA	Rhabdoviridae	11
-ssRNA	Orthomyxoviridae	2
-ssRNA	Chuviridae	1
-ssRNA	Peribunyaviridae	1
dsDNA	Iridoviridae	1
dsRNA	Totiviridae	6
dsRNA	Birnaviridae	1
dsRNA	Partitiviridae	1
ssDNA	Parvoviridae	4
Total	-	66

virus_master_2023 %>% 
  distinct(virus_name, viral_family, .keep_all = TRUE) %>% 
  group_by(genome, viral_family) %>% 
  summarise(n = n()) %>% 
  arrange(genome, desc(n)) %>% 
  adorn_totals() %>% 
  gt() %>% 
  cols_label(
    genome = "Genome",
    viral_family = "Family")

Genome	Family	n
+ssRNA	Iflaviridae	13
+ssRNA	Negevirus	8
+ssRNA	Tombusviridae	4
+ssRNA	Dicistroviridae	3
+ssRNA	Flaviviridae	2
+ssRNA	Narnaviridae	2
+ssRNA	Tymoviridae	2
+ssRNA	Virgaviridae	2
+ssRNA	Luteoviridae	1
+ssRNA	Nodaviridae	1
-ssRNA	Rhabdoviridae	11
-ssRNA	Orthomyxoviridae	2
-ssRNA	Chuviridae	1
-ssRNA	Peribunyaviridae	1
dsDNA	Iridoviridae	1
dsRNA	Totiviridae	6
dsRNA	Birnaviridae	1
dsRNA	Partitiviridae	1
ssDNA	Parvoviridae	4
Total	-	66

Novel Viruses

virus_master_2023 %>% 
  distinct(virus_name, viral_family, .keep_all = TRUE) %>% 
  filter(str_detect(virus_name, "Manitoba ")) %>% 
  filter(!str_detect(virus_name, "Manitoba virus")) %>% 
  group_by(genome, viral_family) %>% 
  summarise(n = n()) %>% 
  gt()

viral_family	n
+ssRNA
Dicistroviridae	1
Iflaviridae	2
Narnaviridae	1
Negevirus	3
Tombusviridae	1
Tymoviridae	1
Virgaviridae	1
-ssRNA
Rhabdoviridae	3
dsDNA
Iridoviridae	1
dsRNA
Totiviridae	3

virus_master_2023 %>% 
  distinct(virus_name, viral_family, .keep_all = TRUE) %>% 
  filter(str_detect(virus_name, "Manitoba ")) %>% 
  filter(!str_detect(virus_name, "Manitoba virus")) %>% 
  group_by(genome, virus_name) %>% 
  summarise(n = n()) %>% 
  adorn_totals() %>% 
  gt()

genome	virus_name	n
+ssRNA	Manitoba dicistro-like virus 1	1
+ssRNA	Manitoba iflavirus 1	1
+ssRNA	Manitoba mononega-like virus 1	1
+ssRNA	Manitoba mononega-like virus 2	1
+ssRNA	Manitoba mononega-like virus 3	1
+ssRNA	Manitoba narnavirus 1	1
+ssRNA	Manitoba picorna-like virus 1	1
+ssRNA	Manitoba tombus-like virus 1	1
+ssRNA	Manitoba tymo-like virus 1	1
+ssRNA	Manitoba virgavirus 1	1
-ssRNA	Manitoba Rhabdovirus 1	1
-ssRNA	Manitoba rhabdovirus 2	1
-ssRNA	Manitoba rhabdovirus 3	1
dsDNA	Manitoba iridescent virus 1	1
dsRNA	Manitoba toti-like virus 1	1
dsRNA	Manitoba toti-like virus 2	1
dsRNA	Manitoba toti-like virus 3	1
Total	-	17

Virus Profiles

Below are summaries for each virus detected.

virus_profile_table <- function(virus) {

 virus_table <<-  virus_master_2023 %>% 
  filter(virus_name == virus) %>% 
  #select(-"contig_sequences") %>% 
  summarise(
    num_species = n_distinct(mosquito_species),
    num_contig = n(),
    longest_contig = max(contig_length),
    shortest_contig = min(contig_length),
    avg_nt_id = mean(greatest_identity_percent),
    max_nt_id = max(greatest_identity_percent),
    min_nt_id = min(greatest_identity_percent)
    
  ) %>% 
  gt() %>% 
  cols_label(
    longest_contig = "Max Contig",
    shortest_contig = "Min Contig",
    avg_nt_id = "Average aa Id",
    max_nt_id = "Max aa Id",
    min_nt_id = "Min aa Id",
    num_contig = "n Contigs",
    num_species = "n Species"
  ) %>% 
  tab_header(
    title = paste0("Summary Stats for", " ", virus)
  ) %>% 
    fmt_number(
      columns = 4:last_col(),
      decimals = 2
    )

}

# Arrange df for virus reporting
virus_master_2023 <<- virus_master_2023 %>% 
  mutate(across(.cols = "virus_name",
                ~case_when(grepl("Manitoba", virus_name) & !grepl("Manitoba virus", virus_name) ~ 
                             paste0(., "*"),
                           TRUE ~ .))) %>% 
  arrange(desc(genome)) %>% 
  drop_na(virus_name)

for(virus in unique(virus_master_2023$virus_name)) {

  genome <- virus_master_2023 %>% 
    arrange(desc(genome)) %>% 
    drop_na(virus_name) %>%  
    filter(virus_name == virus) %>% 
    pull(genome) %>% 
    head(1)
  
  genome <- paste0(genome)
  
  family <- virus_master_2023 %>% 
    filter(virus_name == virus) %>% 
    pull(viral_family) %>% 
    head(1)
  
  family <- paste0(family)

  sample_detections <- virus_master_2023 %>% 
    filter(virus_name == virus) %>% 
    distinct(sample_number)
  sample_detections <- paste0(nrow(sample_detections))
  
  
  cat('\n\n##', virus, '\n\n')
  
  cat('\n\n>', virus, 'has a ', genome, 'genome and is a member of the family', family, 'and was detected in', sample_detections, 'sample(s).', 'See summary figures and tables below.',  '\n\n')
  
print(suppressMessages(
  virus_master_2023 %>% 
    filter(virus_name == virus) %>% 
    select(-"contig_sequence") %>% 
    group_by(mosquito_species, collection_year, location_pool) %>% 
    summarise(n = n_distinct(sample_number)) %>% 
    ggplot(aes(x = mosquito_species, y = n, fill = location_pool)) +
    geom_col() +
    facet_grid(. ~ collection_year) +
    scale_fill_viridis_d("Location", option = "magma") +
    theme_bw() +
    labs(title = paste0("Number of Virus Detections"),
       subtitle = paste0("For ", virus, " by Year, Species and Location")) +
    theme(plot.title = element_text(size = 16, face = "bold"),
        axis.title.x = element_blank(),
        axis.text.x = element_text(angle = 45, vjust = 0.5))
  ))
  
  cat('\n\n###', 'Years {.unlisted .unnumbered}', '\n\n')

  print(htmltools::tagList(
    virus_master_2023 %>% 
      filter(virus_name == virus) %>% 
      group_by(collection_year) %>% 
      summarise(n = n_distinct(sample_number)) %>% 
      gt() %>% 
      cols_label(collection_year = "Year(s) Detected")
    ))
  
  cat('\n\n###', 'Locations {.unlisted .unnumbered}', '\n\n')
  
    print(htmltools::tagList(
    virus_master_2023 %>% 
      filter(virus_name == virus) %>% 
      group_by(location_pool) %>% 
      summarise(n = n_distinct(sample_number)) %>% 
      gt() %>% 
      cols_label(location_pool = "Location(s) Detected")
    ))
    
    cat('\n\n###', 'Mosquito Species {.unlisted .unnumbered}', '\n\n')
  
    print(htmltools::tagList(
    virus_master_2023 %>% 
      filter(virus_name == virus) %>% 
      group_by(mosquito_species) %>% 
      summarise(n = n_distinct(sample_number)) %>% 
      gt() %>% 
      cols_label(mosquito_species = "Mosquito Hosts")
    ))
    
    cat('\n\n###', 'Contig Summary {.unlisted .unnumbered}', '\n\n')

  virus_profile_table(virus)
  
  print(htmltools::tagList(virus_table))
  
  cat('\n\n###', 'aa Identity Summary {.unlisted .unnumbered}', '\n\n')
  
  print(suppressMessages(
  virus_master_2023 %>% 
    filter(virus_name == virus) %>% 
    select(-"contig_sequence") %>% 
    ggplot(aes(x = greatest_identity_percent)) +
    geom_histogram(aes(fill = greatest_identity_percent < 85)) +
    geom_vline(xintercept = 85, linetype = "dotted", colour = "firebrick") +
    theme_bw() +
    labs(title = paste0("aa Identity"),
       subtitle = paste0("For ", virus),
       x = "aa Identity", 
       y = "Number of Contigs") +
    theme(plot.title = element_text(size = 16, face = "bold"),
        axis.title.x = element_blank(),
        axis.text.x = element_text(angle = 45, vjust = 0.5)) +
    theme(legend.position = "none")
  ))
  
}

Culex densovirus

Culex densovirus has a ssDNA genome and is a member of the family Parvoviridae and was detected in 6 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3
2021	3

Locations

Location(s) Detected	n
Cypress River	3
Cypress River & Carberry	1
Shoal Lake	1
Western MB	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	1
Coquillettidia perturbans	4
Culex tarsalis	1

Contig Summary

Summary Stats for Culex densovirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
3	8	1697	393.00	99.56	100.00	97.71

aa Identity Summary

Aedes albopictus densovirus

Aedes albopictus densovirus has a ssDNA genome and is a member of the family Parvoviridae and was detected in 3 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	3

Locations

Location(s) Detected	n
Cypress River	2
Virden	1

Mosquito Species

Mosquito Hosts	n
Coquillettidia perturbans	2
Culex tarsalis	1

Contig Summary

Summary Stats for Aedes albopictus densovirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	4	3355	323.00	97.46	100.00	89.86

aa Identity Summary

Aedes vexans densovirus isolate

Aedes vexans densovirus isolate has a ssDNA genome and is a member of the family Parvoviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Cypress River	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	1

Contig Summary

Summary Stats for Aedes vexans densovirus isolate
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	3367	3,367.00	100.00	100.00	100.00

aa Identity Summary

Grus japonensis parvoviridae

Grus japonensis parvoviridae has a ssDNA genome and is a member of the family Parvoviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Cypress River	1

Mosquito Species

Mosquito Hosts	n
Coquillettidia perturbans	1

Contig Summary

Summary Stats for Grus japonensis parvoviridae
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	570	570.00	100.00	100.00	100.00

aa Identity Summary

Snelk virus

Snelk virus has a dsRNA genome and is a member of the family Totiviridae and was detected in 4 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3
2021	1

Locations

Location(s) Detected	n
Brandon	1
Carberry	1
Cypress River & Carberry	1
Shoal Lake, Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	4

Contig Summary

Summary Stats for Snelk virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	4	295	262.00	100.00	100.00	100.00

aa Identity Summary

Partitivirus-like Culex mosquito virus

Partitivirus-like Culex mosquito virus has a dsRNA genome and is a member of the family Partitiviridae and was detected in 11 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	5
2021	6

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	1
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	11

Contig Summary

Summary Stats for Partitivirus-like Culex mosquito virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	12	1751	299.00	100.00	100.00	100.00

aa Identity Summary

Gouley virus

Gouley virus has a dsRNA genome and is a member of the family Totiviridae and was detected in 3 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3

Locations

Location(s) Detected	n
Brandon	1
Cypress River & Carberry	1
Shoal Lake, Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	3

Contig Summary

Summary Stats for Gouley virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	3	368	263.00	95.04	97.67	92.86

aa Identity Summary

Manitoba toti-like virus 1*

Manitoba toti-like virus 1* has a dsRNA genome and is a member of the family Totiviridae and was detected in 5 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	2
2021	3

Locations

Location(s) Detected	n
Brandon	1
Cypress River	1
Shoal Lake	3

Mosquito Species

Mosquito Hosts	n
Aedes vexans	2
Culex tarsalis	3

Contig Summary

Summary Stats for Manitoba toti-like virus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	5	8930	2,012.00	69.92	73.11	67.43

aa Identity Summary

Ballard Lake virus

Ballard Lake virus has a dsRNA genome and is a member of the family Birnaviridae and was detected in 26 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	10
2021	16

Locations

Location(s) Detected	n
Boissevain	2
Brandon	4
Carberry	1
Cypress River	3
Cypress River & Carberry	1
Killarney	2
Newdale	1
Shoal Lake	5
Souris	2
Virden	2
Virden & Souris	1
WPG Insect Contol	2

Mosquito Species

Mosquito Hosts	n
Aedes vexans	19
Coquillettidia perturbans	4
Culex tarsalis	2
Ochlerotatus dorsalis	1

Contig Summary

Summary Stats for Ballard Lake virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
4	48	3472	707.00	99.86	100.00	93.27

aa Identity Summary

Manitoba toti-like virus 2*

Manitoba toti-like virus 2* has a dsRNA genome and is a member of the family Totiviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Brandon	1

Mosquito Species

Mosquito Hosts	n
Aedes canadensis	1

Contig Summary

Summary Stats for Manitoba toti-like virus 2*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	3123	3,123.00	60.24	60.24	60.24

aa Identity Summary

Hattula totivirus 1

Hattula totivirus 1 has a dsRNA genome and is a member of the family Totiviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
Multiple	1

Mosquito Species

Mosquito Hosts	n
Ochlerotatus triseriatus	1

Contig Summary

Summary Stats for Hattula totivirus 1
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	4909	4,909.00	89.07	89.07	89.07

aa Identity Summary

Manitoba toti-like virus 3*

Manitoba toti-like virus 3* has a dsRNA genome and is a member of the family Totiviridae and was detected in 4 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	4

Locations

Location(s) Detected	n
Boissevain & Killarney	1
Brandon	1
Shoal Lake	1
Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Ochlerotatus dorsalis	4

Contig Summary

Summary Stats for Manitoba toti-like virus 3*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	4	4626	1,821.00	73.53	74.90	72.22

aa Identity Summary

Manitoba iridescent virus 1*

Manitoba iridescent virus 1* has a dsDNA genome and is a member of the family Iridoviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Cypress River	1

Mosquito Species

Mosquito Hosts	n
Coquillettidia perturbans	1

Contig Summary

Summary Stats for Manitoba iridescent virus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	797	797.00	78.74	78.74	78.74

aa Identity Summary

Riverside virus 1

Riverside virus 1 has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 15 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	6
2021	9

Locations

Location(s) Detected	n
Boissevain	1
Brandon	2
Cypress River	1
Cypress River & Carberry	1
Killarney	1
Newdale	1
Shoal Lake	4
Souris	1
Virden	1
Virden & Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	14
Ochlerotatus dorsalis	1

Contig Summary

Summary Stats for Riverside virus 1
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	17	8033	718.00	90.20	93.01	85.32

aa Identity Summary

Chuvirus

Chuvirus has a -ssRNA genome and is a member of the family Chuviridae and was detected in 21 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	9
2021	12

Locations

Location(s) Detected	n
Boissevain	2
Boissevain & Killarney	1
Brandon	3
Carberry	2
Cypress River	1
Cypress River & Carberry	1
Killarney	1
Newdale	1
Shoal Lake	6
Souris	1
Virden	1
Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	17
Culex tarsalis	1
Ochlerotatus dorsalis	3

Contig Summary

Summary Stats for Chuvirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
3	39	6799	433.00	97.49	100.00	89.66

aa Identity Summary

Merida virus

Merida virus has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 11 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	5
2021	6

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	1
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	11

Contig Summary

Summary Stats for Merida virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	55	7483	262.00	99.86	100.00	97.14

aa Identity Summary

Wuhan mosquito virus 6

Wuhan mosquito virus 6 has a -ssRNA genome and is a member of the family Orthomyxoviridae and was detected in 14 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	7
2021	7

Locations

Location(s) Detected	n
Boissevain	1
Brandon	4
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	2
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1
Western MB	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	2
Coquillettidia perturbans	1
Culex tarsalis	11

Contig Summary

Summary Stats for Wuhan mosquito virus 6
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
3	101	2467	252.00	99.76	100.00	97.69

aa Identity Summary

Manitoba rhabdovirus 3*

Manitoba rhabdovirus 3* has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 5 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1
2021	4

Locations

Location(s) Detected	n
Brandon	2
Carberry	1
Cypress River & Carberry	1
Souris	1

Mosquito Species

Mosquito Hosts	n
Aedes canadensis	1
Culex tarsalis	4

Contig Summary

Summary Stats for Manitoba rhabdovirus 3*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	5	6071	587.00	80.94	84.85	66.04

aa Identity Summary

Flanders hapavirus

Flanders hapavirus has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 13 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	5
2021	8

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	3
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	3
Culex tarsalis	10

Contig Summary

Summary Stats for Flanders hapavirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	81	8773	263.00	99.90	100.00	95.96

aa Identity Summary

Astopletus virus

Astopletus virus has a -ssRNA genome and is a member of the family Orthomyxoviridae and was detected in 11 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	5
2021	6

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	1
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	11

Contig Summary

Summary Stats for Astopletus virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	29	1044	464.00	99.06	100.00	95.77

aa Identity Summary

Elisy virus

Elisy virus has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 5 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3
2021	2

Locations

Location(s) Detected	n
Brandon	3
Cypress River & Carberry	1
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	5

Contig Summary

Summary Stats for Elisy virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	21	1817	373.00	99.27	100.00	96.41

aa Identity Summary

Culex Rhabdo-like virus

Culex Rhabdo-like virus has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 3 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1
2021	2

Locations

Location(s) Detected	n
Brandon	1
Cypress River & Carberry	1
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	3

Contig Summary

Summary Stats for Culex Rhabdo-like virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	4	1973	672.00	100.00	100.00	100.00

aa Identity Summary

Culex bunyavirus 2

Culex bunyavirus 2 has a -ssRNA genome and is a member of the family Peribunyaviridae and was detected in 11 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	5
2021	6

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	1
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	11

Contig Summary

Summary Stats for Culex bunyavirus 2
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	19	1896	350.00	100.00	100.00	100.00

aa Identity Summary

Canya virus

Canya virus has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 7 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3
2021	4

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Cypress River	1
Shoal Lake	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	7

Contig Summary

Summary Stats for Canya virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	9	2444	522.00	90.87	100.00	85.05

aa Identity Summary

Manitoba virus

Manitoba virus has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	1

Contig Summary

Summary Stats for Manitoba virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	5	1589	500.00	99.76	100.00	98.80

aa Identity Summary

Culex rhabdovirus

Culex rhabdovirus has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 2 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	2

Locations

Location(s) Detected	n
Brandon	1
Cypress River	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	2

Contig Summary

Summary Stats for Culex rhabdovirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	2	429	359.00	100.00	100.00	100.00

aa Identity Summary

Manitoba Rhabdovirus 1*

Manitoba Rhabdovirus 1* has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 15 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	7
2021	8

Locations

Location(s) Detected	n
Boissevain	1
Brandon	2
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Killarney	2
Newdale	1
Shoal Lake	3
Souris	1
Virden	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	14
Ochlerotatus dorsalis	1

Contig Summary

Summary Stats for Manitoba Rhabdovirus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	20	5085	784.00	77.30	83.33	69.42

aa Identity Summary

Manitoba rhabdovirus 2*

Manitoba rhabdovirus 2* has a -ssRNA genome and is a member of the family Rhabdoviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	1

Contig Summary

Summary Stats for Manitoba rhabdovirus 2*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	4648	4,648.00	75.00	75.00	75.00

aa Identity Summary

Yongsan picorna-like virus 1

Yongsan picorna-like virus 1 has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 21 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	10
2021	11

Locations

Location(s) Detected	n
Boissevain	1
Boissevain & Killarney	1
Brandon	4
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Killarney	2
Newdale	1
Shoal Lake	5
Souris	1
Virden	1
Virden & Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	18
Ochlerotatus dorsalis	3

Contig Summary

Summary Stats for Yongsan picorna-like virus 1
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	64	4085	510.00	89.40	100.00	85.05

aa Identity Summary

Hanko iflavirus 1

Hanko iflavirus 1 has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 12 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	8
2021	4

Locations

Location(s) Detected	n
Boissevain & Killarney	1
Brandon	1
Cypress River	1
Newdale	1
Shoal Lake	4
Virden & Souris	1
WPG Insect Contol	3

Mosquito Species

Mosquito Hosts	n
Aedes vexans	4
Coquillettidia perturbans	1
Culex tarsalis	1
Ochlerotatus dorsalis	5
Ochlerotatus flavescens	1

Contig Summary

Summary Stats for Hanko iflavirus 1
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
5	30	9246	308.00	97.49	100.00	93.45

aa Identity Summary

Pedersore iflavirus

Pedersore iflavirus has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 17 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	16
2021	1

Locations

Location(s) Detected	n
Boissevain & Killarney	1
Brandon	5
Cypress River & Carberry	2
Killarney	1
Shoal Lake	4
Virden & Souris	1
WPG Insect Contol	2
Western MB	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	7
Coquillettidia perturbans	2
Culex tarsalis	3
Ochlerotatus dorsalis	4
Ochlerotatus flavescens	1

Contig Summary

Summary Stats for Pedersore iflavirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
5	25	9899	286.00	93.47	100.00	89.14

aa Identity Summary

Marma virus

Marma virus has a +ssRNA genome and is a member of the family Luteoviridae and was detected in 12 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	6
2021	6

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	1
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1
Western MB	1

Mosquito Species

Mosquito Hosts	n
Coquillettidia perturbans	1
Culex tarsalis	11

Contig Summary

Summary Stats for Marma virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	23	3160	1,574.00	100.00	100.00	100.00

aa Identity Summary

Culex iflavilike virus 3

Culex iflavilike virus 3 has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 11 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	5
2021	6

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	1
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	11

Contig Summary

Summary Stats for Culex iflavilike virus 3
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	183	1824	250.00	99.49	100.00	94.19

aa Identity Summary

Placeda virus

Placeda virus has a +ssRNA genome and is a member of the family Flaviviridae and was detected in 13 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	6
2021	7

Locations

Location(s) Detected	n
Boissevain	1
Brandon	4
Carberry	1
Cypress River	1
Cypress River & Carberry	1
Shoal Lake	2
Shoal Lake, Virden & Souris	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	2
Culex tarsalis	11

Contig Summary

Summary Stats for Placeda virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	169	11737	252.00	97.87	100.00	86.24

aa Identity Summary

Culex Iflavi-like virus 4

Culex Iflavi-like virus 4 has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 7 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	4
2021	3

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River & Carberry	1
Shoal Lake, Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	7

Contig Summary

Summary Stats for Culex Iflavi-like virus 4
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	23	9811	285.00	99.81	100.00	96.20

aa Identity Summary

Hubei mosquito virus 4

Hubei mosquito virus 4 has a +ssRNA genome and is a member of the family Tombusviridae and was detected in 6 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3
2021	3

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Carberry	1
Cypress River & Carberry	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	6

Contig Summary

Summary Stats for Hubei mosquito virus 4
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	6	5103	367.00	96.50	100.00	92.65

aa Identity Summary

Hubei virga-like virus 2

Hubei virga-like virus 2 has a +ssRNA genome and is a member of the family Virgaviridae and was detected in 4 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3
2021	1

Locations

Location(s) Detected	n
Brandon	2
Cypress River & Carberry	1
Souris	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	4

Contig Summary

Summary Stats for Hubei virga-like virus 2
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	6	947	290.00	99.04	100.00	96.27

aa Identity Summary

Des Moines River virus

Des Moines River virus has a +ssRNA genome and is a member of the family Tombusviridae and was detected in 4 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	4

Locations

Location(s) Detected	n
Brandon	3
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	1
Culex tarsalis	3

Contig Summary

Summary Stats for Des Moines River virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	4	2361	1,070.00	100.00	100.00	100.00

aa Identity Summary

Manitoba dicistro-like virus 1*

Manitoba dicistro-like virus 1* has a +ssRNA genome and is a member of the family Dicistroviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
Brandon	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	1

Contig Summary

Summary Stats for Manitoba dicistro-like virus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	7146	7,146.00	82.61	82.61	82.61

aa Identity Summary

Soybean thrips dicistrovirus

Soybean thrips dicistrovirus has a +ssRNA genome and is a member of the family Dicistroviridae and was detected in 9 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3
2021	6

Locations

Location(s) Detected	n
Boissevain	2
Brandon	1
Carberry	1
Newdale	1
Shoal Lake	2
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	3
Culex tarsalis	5
Ochlerotatus dorsalis	1

Contig Summary

Summary Stats for Soybean thrips dicistrovirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
3	11	9121	893.00	100.00	100.00	100.00

aa Identity Summary

Yongsan picorna-like virus 2

Yongsan picorna-like virus 2 has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 3 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1
2021	2

Locations

Location(s) Detected	n
Brandon	2
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	3

Contig Summary

Summary Stats for Yongsan picorna-like virus 2
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	4	9573	2,367.00	100.00	100.00	100.00

aa Identity Summary

Manitoba tombus-like virus 1*

Manitoba tombus-like virus 1* has a +ssRNA genome and is a member of the family Tombusviridae and was detected in 5 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	3
2021	2

Locations

Location(s) Detected	n
Brandon	2
Shoal Lake	1
Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	5

Contig Summary

Summary Stats for Manitoba tombus-like virus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	5	2340	1,687.00	75.68	76.92	72.73

aa Identity Summary

Culex narnavirus 1

Culex narnavirus 1 has a +ssRNA genome and is a member of the family Narnaviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
Brandon	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	1

Contig Summary

Summary Stats for Culex narnavirus 1
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	513	513.00	100.00	100.00	100.00

aa Identity Summary

Hubei noda-like virus 12

Hubei noda-like virus 12 has a +ssRNA genome and is a member of the family Nodaviridae and was detected in 2 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	2

Locations

Location(s) Detected	n
Carberry	1
Virden	1

Mosquito Species

Mosquito Hosts	n
Coquillettidia perturbans	1
Culex tarsalis	1

Contig Summary

Summary Stats for Hubei noda-like virus 12
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	2	4762	841.00	95.83	100.00	91.67

aa Identity Summary

Manitoba mononega-like virus 1*

Manitoba mononega-like virus 1* has a +ssRNA genome and is a member of the family Negevirus and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Brandon	1

Mosquito Species

Mosquito Hosts	n
Aedes canadensis	1

Contig Summary

Summary Stats for Manitoba mononega-like virus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	11180	11,180.00	73.21	73.21	73.21

aa Identity Summary

Bro virus

Bro virus has a +ssRNA genome and is a member of the family Negevirus and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Brandon	1

Mosquito Species

Mosquito Hosts	n
Aedes canadensis	1

Contig Summary

Summary Stats for Bro virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	11375	11,375.00	90.00	90.00	90.00

aa Identity Summary

Manitoba mononega-like virus 2*

Manitoba mononega-like virus 2* has a +ssRNA genome and is a member of the family Negevirus and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Brandon	1

Mosquito Species

Mosquito Hosts	n
Aedes canadensis	1

Contig Summary

Summary Stats for Manitoba mononega-like virus 2*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	2477	2,477.00	75.00	75.00	75.00

aa Identity Summary

Hubei macula-like virus 3

Hubei macula-like virus 3 has a +ssRNA genome and is a member of the family Tymoviridae and was detected in 5 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	4
2021	1

Locations

Location(s) Detected	n
Brandon	2
Shoal Lake	2
Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	4
Ochlerotatus dorsalis	1

Contig Summary

Summary Stats for Hubei macula-like virus 3
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	8	6059	2,954.00	96.13	100.00	92.15

aa Identity Summary

Hanko iflavirus 2

Hanko iflavirus 2 has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 13 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	9
2021	4

Locations

Location(s) Detected	n
Boissevain	1
Brandon	3
Cypress River & Carberry	1
Killarney	1
Shoal Lake	4
Souris	1
Virden & Souris	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	11
Coquillettidia perturbans	1
Ochlerotatus dorsalis	1

Contig Summary

Summary Stats for Hanko iflavirus 2
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
3	16	9206	461.00	97.05	100.00	89.58

aa Identity Summary

Black queen cell virus

Black queen cell virus has a +ssRNA genome and is a member of the family Dicistroviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
Brandon	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	1

Contig Summary

Summary Stats for Black queen cell virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	2	6035	2,087.00	100.00	100.00	100.00

aa Identity Summary

Manitoba picorna-like virus 1*

Manitoba picorna-like virus 1* has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 12 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	7
2021	5

Locations

Location(s) Detected	n
Boissevain	2
Brandon	2
Cypress River & Carberry	1
Killarney	2
Newdale	1
Shoal Lake	3
Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	12

Contig Summary

Summary Stats for Manitoba picorna-like virus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	20	2114	573.00	81.99	84.96	73.93

aa Identity Summary

Cordoba virus

Cordoba virus has a +ssRNA genome and is a member of the family Negevirus and was detected in 3 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	3

Locations

Location(s) Detected	n
Boissevain	1
Cypress River	1
Souris	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	3

Contig Summary

Summary Stats for Cordoba virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	14	5133	610.00	97.10	100.00	93.75

aa Identity Summary

Mekrijarvi Negevirus

Mekrijarvi Negevirus has a +ssRNA genome and is a member of the family Negevirus and was detected in 6 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	2
2021	4

Locations

Location(s) Detected	n
Boissevain	1
Boissevain & Killarney	1
Cypress River	1
Shoal Lake	1
Souris	1
Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	3
Ochlerotatus dorsalis	3

Contig Summary

Summary Stats for Mekrijarvi Negevirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	6	9873	3,125.00	94.13	100.00	90.78

aa Identity Summary

Big Cypress virus

Big Cypress virus has a +ssRNA genome and is a member of the family Negevirus and was detected in 3 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1
2021	2

Locations

Location(s) Detected	n
Boissevain	1
Brandon	1
Souris	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	3

Contig Summary

Summary Stats for Big Cypress virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	3	9570	2,735.00	98.77	100.00	96.30

aa Identity Summary

Manitoba mononega-like virus 3*

Manitoba mononega-like virus 3* has a +ssRNA genome and is a member of the family Negevirus and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
Multiple	1

Mosquito Species

Mosquito Hosts	n
Ochlerotatus triseriatus	1

Contig Summary

Summary Stats for Manitoba mononega-like virus 3*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	5456	5,456.00	78.57	78.57	78.57

aa Identity Summary

Manitoba iflavirus 1*

Manitoba iflavirus 1* has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 10 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	5
2021	5

Locations

Location(s) Detected	n
Boissevain	1
Brandon	1
Killarney	1
Newdale	1
Shoal Lake	3
Souris	1
Virden	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	9
Ochlerotatus dorsalis	1

Contig Summary

Summary Stats for Manitoba iflavirus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	13	2435	573.00	78.42	83.54	67.08

aa Identity Summary

Tiger mosquito bi-segmented tombus-like virus

Tiger mosquito bi-segmented tombus-like virus has a +ssRNA genome and is a member of the family Tombusviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Souris	1

Mosquito Species

Mosquito Hosts	n
Culex tarsalis	1

Contig Summary

Summary Stats for Tiger mosquito bi-segmented tombus-like virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	2351	2,351.00	100.00	100.00	100.00

aa Identity Summary

Hubei arthropod virus 1

Hubei arthropod virus 1 has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	1

Contig Summary

Summary Stats for Hubei arthropod virus 1
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	2967	2,967.00	100.00	100.00	100.00

aa Identity Summary

Thrace picorna-like virus 1

Thrace picorna-like virus 1 has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 2 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	2

Locations

Location(s) Detected	n
Cypress River	1
Newdale	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	2

Contig Summary

Summary Stats for Thrace picorna-like virus 1
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	2	1172	1,115.00	91.62	93.65	89.58

aa Identity Summary

Soybean thrips iflavirus 4

Soybean thrips iflavirus 4 has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Coquillettidia perturbans	1

Contig Summary

Summary Stats for Soybean thrips iflavirus 4
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	3835	3,835.00	100.00	100.00	100.00

aa Identity Summary

Cafluga virus

Cafluga virus has a +ssRNA genome and is a member of the family Iflaviridae and was detected in 2 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	2

Locations

Location(s) Detected	n
Boissevain & Killarney	1
WPG Insect Contol	1

Mosquito Species

Mosquito Hosts	n
Coquillettidia perturbans	1
Ochlerotatus dorsalis	1

Contig Summary

Summary Stats for Cafluga virus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
2	2	3426	1,395.00	99.77	100.00	99.55

aa Identity Summary

Manitoba tymo-like virus 1*

Manitoba tymo-like virus 1* has a +ssRNA genome and is a member of the family Tymoviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Boissevain	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	1

Contig Summary

Summary Stats for Manitoba tymo-like virus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	6302	6,302.00	66.79	66.79	66.79

aa Identity Summary

Utsjoki negevirus 3

Utsjoki negevirus 3 has a +ssRNA genome and is a member of the family Negevirus and was detected in 2 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	2

Locations

Location(s) Detected	n
Shoal Lake	1
Virden & Souris	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	2

Contig Summary

Summary Stats for Utsjoki negevirus 3
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	2	989	972.00	99.02	99.03	99.01

aa Identity Summary

Inari jingmenvirus

Inari jingmenvirus has a +ssRNA genome and is a member of the family Flaviviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Aedes vexans	1

Contig Summary

Summary Stats for Inari jingmenvirus
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	1267	1,267.00	100.00	100.00	100.00

aa Identity Summary

Manitoba virgavirus 1*

Manitoba virgavirus 1* has a +ssRNA genome and is a member of the family Virgaviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2020	1

Locations

Location(s) Detected	n
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Ochlerotatus dorsalis	1

Contig Summary

Summary Stats for Manitoba virgavirus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	1	1675	1,675.00	83.83	83.83	83.83

aa Identity Summary

Manitoba narnavirus 1*

Manitoba narnavirus 1* has a +ssRNA genome and is a member of the family Narnaviridae and was detected in 1 sample(s). See summary figures and tables below.

Years

Year(s) Detected	n
2021	1

Locations

Location(s) Detected	n
Shoal Lake	1

Mosquito Species

Mosquito Hosts	n
Anopheles earlei	1

Contig Summary

Summary Stats for Manitoba narnavirus 1*
n Species	n Contigs	Max Contig	Min Contig	Average aa Id	Max aa Id	Min aa Id
1	2	1760	654.00	80.59	80.89	80.29

aa Identity Summary